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Academic Workflow - Any Suggestion for an Application/s?

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Posted by Matthias Steffens
Jan 22, 2020 at 11:49 PM


Darren McDonald wrote:
>I am trying to decide on an application to use when reading PDFs,
>making annotations and taking notes.

>Another thing I am trying to do is find an application that helps me
>bring together the annotations and notes to find themes and decide
>where I use them in a journal article. Any suggestions on what application
>to use to do this?

Like others in this thread, I can definitely recommend Citavi (https://citavi.com) for this. It’s a great product, made by fine people, and has oustanding support. But don’t take my word for it, I’m probably biased since I’ve worked for them (I was once tasked to develop Citavi for Mac but this ultimately didn’t work out, unfortunately). But I recommend to try it out yourself.

Users trying to implement an academic reading & notetaking workflow on the Mac usually have to combine apps from at least these three categories: PDF highlighting, note taking and reference management. Trying to integrate apps from these categories usually means a lot of back & forth or scripting/automation.

Trying to ease such an academic workflow on the Mac, I’ve started to develop my own app (https://keypoints.app) for personal info & knowledge management. [It is my hope that this doesn’t come across as pure self-promotion, but that participants in this thread may find it actually interesting, and may even offer some feedback on the app’s intended workflow.]

My app tries to sit in between the three above mentioned categories and offer a little bit of all of them: While highlighting your PDF, the app extracts each highlight annotation as a self-standing plaintext/MultiMarkdown note, and can include bibliographic information.

In each note, the app includes the highlighted text as a quotation, adds page information and (if possible) fetches reference info (citekey, formatted reference & DOI) from your reference manager. You can then add your own title/summary/comments to the note, assign it a color label, tag or rate it, and link it with other notes (all via drag & drop or autocompletion). These structural elements get syntax colored and are clickable so you can easily navigate your network of notes. Note connections can be visualized in a network graph (which can also be used for navigation).

Since all your highlight annotations are self-contained plaintext notes, you can search and filter them freely, and gather them again in structure/overview notes. Selecting a note will also jump to its quoted text in the PDF. And clicking a highlight annotation in the PDF will select its note.

I plan to auto-export all notes to disk, which will help to avoid lock-in and should enable basic integration with other apps/services. The app is also highly scriptable, and I’d like to develop custom export/sync scripts to facilitate good integration with other scriptable apps such as DEVONthink, Tinderbox, OmniOutliner, Papers or Bookends etc.

The app is still in development and unfortunately not yet available as a (beta) release. But the Keypoints forums contain more info about its development progress (which could be faster). The latest status report (https://keypoints.app/forums/viewtopic.php?f=2&t=35) also offers a short screencast which shows the app in action.

I’m very interested to hear if an app like this could be part of your academic workflow. Thanks, Matthias